Some injections do sting a bit and she was obviously stressed. And concerning vaccines in the future - my vet was giving one of my girls an injection of some kind recently and was giving it in the rear area. I had been taught to do any sub-q injection in the neck and asked him about it and if it was because of SM. He said that studies have shown that the medication is absorbed much more readily if given in the rear than in the skin around the neck. I certainly wouldn't feel shy about talking to the vet about it.
Glad all is doing better with your baby. We went through a bout of hemorrhagic gastoenteritis a couple of years ago and thought we were going to lose Tibby.
Does your dog like yogurt? You might want to try some plain yogurt on her dinner -- if she has a bad bacteria in her gut, the yogurt could help by repopulating with the good bacteria. Also, antibiotics do wipe out the good intestinal flora as well as the bad, so you might want to try yogurt or a probiotic.
When Butter had a nasty bout of some kind of bad bacteria in his gut last fall (eating treasures in the field left by the wildlife), he had severe diarrhea and vomiting. Apparently the toxins produced by the bacteria affected his neurological system because he couldn't get off his bed or walk very well until it passed. The yogurt did help him and the whole incident put numerous gray hairs on my head.
Hope your little one is feeling better soon.